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I checked this (to keep from having too many capture files in screenshot folder) but still all my captured files get saved in the screenshots folder before I even get a chance to do it in my ext. editor. What am I doing wrong?

One possibility is that you have an option set which *requires* the image to be saved each time. For example if you have an option set to copy each screenshot's file name to the clipboard after a screencapture, that would do it.